Hi there! I am a Masters student and this is my first email to the list. I would just like to ask whether someone can clarify something for me regarding the index .ndx files. I am using an nvt.mdp file in order to run an nvt equilibration step. The section of interest is the following (currently receiving an error):
### ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = CX ssdna; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ### The current error says that a number of atoms are not part of any of the T-Coupling groups. Therefore I have the following questions: - Does this mean all atoms (including SOL) must be included in the groups specified using 'tc-grps'? - If my index.ndx file is very large (contains > 20 groups), do I have to manually write them down at 'tc-grps' in the mdp file or is there a way to automatically import the groups present in the index.ndx file? Best, Sebastian -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
